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Amber问题-带电荷的小分子antechamber怎样处理

已有 2465 次阅读 2018-6-10 16:32 |系统分类:科研笔记

对于带有电荷的小分子,在使用 antechamber计算电荷的时候,需要使用 -nc flag,具体用法见下面语句,以下内容转载自amber Q&A


http://archive.ambermd.org/201010/0417.html


If the molecule is charged in the system of interest, please use the -nc flag with antechamber as in the example below: 

antechamber -i gdp3.pdb -fi pdb -nc -3 -o gdp3.mol2 -fo mol2 -c bcc -s 2 

Please notice that (page 83, AmberTools 11 manual) "Also note that this procedure 
depends heavily upon the initial 3D structure: it must have all hydrogens present, and the 
charges computed are those for the conformation you provide, after minimization in the AM1 
Hamiltonian. In fact, this means that you must have an reasonable all-atom initial model of 
your molecule (so that it can be minimized with the AM1 Hamiltonian), and you may need to 
specify what its net charge is, especially for those molecular formats that have no net charge 
information, and no partial charges or the partial charges in the input are not correct. The 
system should really be a closed-shell molecule, since all of the atom-typing rules assume this 
implicitly." 



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